Contacts of the helix formed by residues 257 - 273 (chain A) in PDB entry 6ABP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 4.0 1.2 - - - +
23A PHE* 3.4 50.9 - - + +
255A SER* 3.1 16.5 - - - -
256A PRO* 1.4 76.1 - - - +
258A VAL* 1.3 69.6 + - - +
261A TYR* 3.0 24.3 + - - +
301A LYS* 2.5 46.0 + - - +
303A LEU* 3.9 11.2 - - + +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A SER* 3.0 28.5 + - - +
257A ASP* 1.3 88.3 - - - +
259A HIS* 1.3 65.1 + - + +
261A TYR* 4.9 2.0 - - - -
262A LYS* 2.8 49.5 + - + +
283A VAL* 4.1 24.5 - - + -
285A ASP* 4.1 9.0 - - - +
301A LYS* 4.5 3.4 - - - +
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Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 3.8 13.9 - + - -
20A GLU* 3.5 16.8 + - - +
88A VAL* 3.8 12.6 - - + +
89A ASP* 2.7 26.9 + - - -
106A VAL* 4.3 11.7 - - + -
107A MET* 3.6 5.5 - - - -
108A LEU* 3.4 36.2 + - + +
255A SER 3.0 33.9 + - - -
256A PRO* 3.7 6.5 - - + +
258A VAL* 1.3 79.1 - - - +
260A GLY* 1.3 52.7 + - - +
263A SER* 2.7 37.4 + - - -
283A VAL* 3.8 29.9 - - + +
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.8 9.1 - - - -
20A GLU* 3.4 28.2 - - - +
23A PHE* 4.3 0.7 - - - -
24A ALA* 3.6 9.2 - - - +
256A PRO 2.9 17.4 + - - -
257A ASP 4.0 0.4 - - - -
259A HIS* 1.3 72.6 - - - +
261A TYR* 1.3 61.5 + - - +
263A SER* 3.6 0.9 + - - -
264A SER* 3.0 28.9 + - - -
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.5 34.5 - + + +
26A LYS* 3.9 11.0 - - + -
27A ALA* 3.6 23.1 - - + +
30A ASP* 2.6 37.1 + - - +
31A LEU* 5.3 3.8 - - + +
257A ASP 3.0 16.8 + - - +
258A VAL* 4.3 2.7 - - - +
260A GLY* 1.3 77.4 - - - +
262A LYS* 1.4 59.4 + - + +
264A SER* 3.4 1.9 + - - -
265A GLU* 2.7 55.7 + - + +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 5.3 3.6 - - + -
258A VAL* 2.8 38.4 + - + +
259A HIS* 5.1 1.1 - - - -
261A TYR* 1.4 71.9 - - + +
263A SER* 1.3 69.7 - - - +
265A GLU* 3.8 18.8 + - - +
266A MET* 3.0 52.6 + - + +
278A PRO* 6.1 0.9 - - - -
281A THR* 4.0 28.7 - - + -
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.6 19.8 - - - -
62A VAL* 3.7 19.3 - - - +
86A ILE* 3.8 11.9 - - - +
88A VAL* 4.4 3.7 - - - +
106A VAL* 4.1 19.4 - - - +
259A HIS 2.7 25.0 + - - -
262A LYS* 1.3 83.1 - - - +
264A SER* 1.3 56.8 + - - +
266A MET* 3.6 10.5 + - - +
267A LEU* 3.0 27.2 + - - +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.5 0.9 - - - +
7A PHE* 3.5 10.7 - - - -
24A ALA* 3.3 19.7 - - - +
27A ALA* 3.8 15.9 - - - -
33A PHE* 3.9 17.2 - - - -
35A VAL* 5.4 0.7 - - - +
62A VAL* 4.1 6.8 - - - +
260A GLY 3.0 19.7 + - - -
261A TYR 3.6 2.7 - - - -
263A SER* 1.3 76.7 + - - +
265A GLU* 1.4 65.0 + - - +
267A LEU* 3.3 5.3 + - - +
268A TYR* 3.0 24.8 + - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.3 1.0 - - + +
31A LEU* 3.9 26.2 - - + -
261A TYR* 2.7 41.8 + - + +
262A LYS* 3.8 28.3 + - - +
264A SER* 1.4 74.5 - - - +
266A MET* 1.4 58.7 + - + +
268A TYR* 3.4 2.8 + - - +
269A ASN* 2.9 43.5 + - - +
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 3.9 15.2 - - + +
104A PRO* 6.2 0.9 - - + -
106A VAL* 3.3 34.8 - - + -
262A LYS* 3.0 46.9 + - + +
263A SER* 3.8 4.3 - - - +
265A GLU* 1.4 80.6 - - + +
267A LEU* 1.3 63.4 + - - +
269A ASN* 3.5 6.1 + - - +
270A TRP* 3.1 23.6 + - - +
275A VAL 4.5 0.9 - - - +
277A PRO* 4.2 11.2 - - + +
278A PRO* 3.9 33.0 - - + +
281A THR* 4.4 5.6 - - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.1 26.0 - - + -
6A GLY 4.5 0.4 - - - +
60A GLY 3.8 3.6 - - - -
61A PHE* 3.5 36.6 - - - +
62A VAL* 3.9 10.8 - - + +
84A LYS* 3.8 35.4 - - + +
86A ILE* 3.6 23.5 - - + +
263A SER 3.0 18.6 + - - +
264A SER* 3.3 6.9 + - - +
266A MET* 1.3 75.0 - - - +
268A TYR* 1.4 54.8 + - - +
270A TRP* 3.2 6.2 + - + +
271A VAL* 2.8 38.3 + - + +
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.6 27.8 - - + -
5A LEU* 4.0 8.0 - - + +
31A LEU* 3.6 44.0 + - + -
32A GLY 4.5 6.0 + - - -
33A PHE* 3.5 30.5 - + + -
264A SER 3.0 17.1 + - - +
265A GLU 3.6 4.5 - - - +
267A LEU* 1.4 74.7 - - - +
269A ASN* 1.3 73.4 + - - +
271A VAL* 3.2 2.0 + - - +
272A ALA* 2.8 53.6 + - + +
273A LYS* 3.8 17.2 - - - -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.2 3.0 - - - +
265A GLU* 2.9 38.5 + - - +
266A MET* 3.9 7.6 - - - +
267A LEU 3.5 0.2 - - - -
268A TYR* 1.3 80.4 - - - +
270A TRP* 1.3 56.8 + - - +
273A LYS* 2.7 60.5 + - + +
275A VAL* 3.2 31.0 + - + +
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Residues in contact with TRP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.4 53.6 - - + +
85A VAL 3.4 27.1 - - - -
86A ILE* 4.0 12.3 - - + -
102A THR 5.8 0.2 - - - -
104A PRO* 4.0 25.6 - - + -
266A MET 3.1 12.1 + - - +
267A LEU* 3.4 9.0 - - + +
269A ASN* 1.3 74.4 - - - +
271A VAL* 1.3 63.4 + - + +
274A ASP* 2.9 39.3 + - - -
275A VAL 3.0 25.7 + - - +
276A GLU* 3.5 29.8 + - - -
277A PRO* 3.5 18.6 - - + -
279A LYS* 6.3 0.2 - - - -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.8 23.6 - - + -
5A LEU* 4.3 6.3 - - + -
59A LYS* 3.5 48.0 - - + +
84A LYS* 4.0 24.2 - - + -
267A LEU* 2.8 26.9 + - + +
268A TYR* 3.9 2.0 - - - +
270A TRP* 1.3 81.1 - - - +
272A ALA* 1.3 62.6 + - - +
274A ASP 4.5 1.0 + - - -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.6 5.4 - - + -
268A TYR* 2.8 56.4 + - + +
271A VAL* 1.3 76.5 - - - +
273A LYS* 1.3 64.6 + - + +
274A ASP 3.9 0.2 - - - -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.6 3.0 - - - +
268A TYR* 3.8 22.1 - - - -
269A ASN* 2.7 47.1 + - - +
272A ALA* 1.3 79.6 - - + +
274A ASP* 1.3 72.0 + - - +
275A VAL* 2.9 20.4 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il